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stschiff / msmc

Implementation of the multiple sequential markovian coalescent
GNU General Public License v3.0
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mappability mask file #10

Closed BegonaMartinez closed 9 years ago

BegonaMartinez commented 9 years ago

Dear author,

I am starting to prepare the infiles for the analyses of MSMC and I have encountered a difficulty about the mappability_mask file. I am following the indications in Heng's Li SNPable regions web to generate my mask_35_50.fa file (as a starting point I am using the same parameters as Li). Otherwise I cannot see how to transform this mask_35_50.fa file into your mappability_mask.chromosome.bed.txt.gz file. I wanted to have a look to the maks you made for humans in your ftp site as you indicate ("For humans (GRCh37), you can download these masks from my ftp site, see the readme for msmc") but I do not see where in the readme it is indicated how to access to this data Could you give me a hint?

Thanks a lot in advance. Best,

Begona

stschiff commented 9 years ago

Yes, indeed you need a little script to convert the mask from fast to bed format. I upload the script I use to the msmc-tools now. I hope that'll help.